I know you must exit the client before you upload to the website, it's not enough to wait till a census is complete or to just log out to char select. So if your question is 'how far do I have to get before I can upload what I've just done', the answer is 'all the way to desktop'.

But, from what they've told me before, if I'm doing multiple servers/sides, and logging in and out of chars, and I get to a certain char and my client crashes, I've only lost the data from that one character; the rest of the censii I've taken that evening are ok, and I can upload the file and it won't Error out.

That is correct the Blizzard WoW client writes all data that addons request in the .TOC files when the character exits the world via log out. If you crash out of the WoW client then any new data that you might have saved is lost since the write out never had a chance to happen.

Also if you log out while a census run is in progress.. any character updates you see before the log out finishes is recorded... but the final summation of the counts don't happen so you don't get credit for doing the census run on that realm/faction ( and the character activity graphs don't get the data they need for updates.)

When you start the WoW client it scans all the sub-folders of the Interface folder (this is where the addon code lives) looking for .TOC files and it reads the directives at that time, and only at that time. This is why if you add a new addon, you need to shutdown and restart the WoW client.

When you log into a character, the WoW client opens up and reads the program files in those sub-folders according to the instructions in the .TOC files. One of the things that addon programmers need to handle is tracking when the client sends of the message that the addon code has been loaded.. and then later the client sends another message when the saved data has been reloaded back into the client.